SGCG

sarcoglycan gamma

Basic information

Region (hg38): 13:23180979-23325162

Previous symbols: [ "DMDA1", "MAM", "LGMD2C" ]

Links

ENSG00000102683 ∙ NCBI:6445 ∙ OMIM:608896 ∙ HGNC:10809 ∙ Uniprot:Q13326 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive limb-girdle muscular dystrophy type 2C (Definitive), mode of inheritance: AR
• autosomal recessive limb-girdle muscular dystrophy type 2C (Strong), mode of inheritance: AR
• autosomal recessive limb-girdle muscular dystrophy type 2C (Supportive), mode of inheritance: AR
• autosomal recessive limb-girdle muscular dystrophy type 2C (Definitive), mode of inheritance: AR
• autosomal recessive limb-girdle muscular dystrophy (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Muscular dystrophy, limb-girdle, limb-girdle, autosomal recessive, 5	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal	1303286; 7481775; 8923014; 8968757; 10507732; 10720277; 16832103; 18285821

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SGCG gene.

• Autosomal_recessive_limb-girdle_muscular_dystrophy_type_2C (451 variants)
• not_provided (112 variants)
• not_specified (26 variants)
• Inborn_genetic_diseases (24 variants)
• Sarcoglycanopathy (15 variants)
• Autosomal_recessive_limb-girdle_muscular_dystrophy (13 variants)
• SGCG-related_disorder (11 variants)
• Limb-girdle_muscular_dystrophy,_recessive (4 variants)
• Abnormality_of_the_musculature (1 variants)
• Primary_dilated_cardiomyopathy (1 variants)
• Proximal_muscle_weakness (1 variants)
• SGCG-related_congenital_myopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SGCG gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000231.3. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			11	110	1	122
missense	3	8	157	8		176
nonsense	9	15	1			25
start loss						0
frameshift	25	21				46
splice donor/acceptor (+/-2bp)	7	19	1			27
Total	44	63	170	118	1

Highest pathogenic variant AF is 0.00009232157

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SGCG	protein_coding	protein_coding	ENST00000218867	7	144214

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000482	0.876	125705	0	43	125748	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.134	168	163	1.03	0.00000874	1881
Missense in Polyphen		64	65.214	0.98139		773
Synonymous	-1.14	73	61.6	1.18	0.00000359	562
Loss of Function	1.44	9	15.0	0.600	7.03e-7	180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000667	0.000666
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000193	0.000193
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000989	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the sarcoglycan complex, a subcomplex of the dystrophin-glycoprotein complex which forms a link between the F-actin cytoskeleton and the extracellular matrix.
• Pathway: Dilated cardiomyopathy (DCM) - Homo sapiens (human);Viral myocarditis - Homo sapiens (human);Arrhythmogenic right ventricular cardiomyopathy (ARVC) - Homo sapiens (human);Hypertrophic cardiomyopathy (HCM) - Homo sapiens (human);Arrhythmogenic Right Ventricular Cardiomyopathy (Consensus)

Recessive Scores

• pRec: 0.363

Intolerance Scores

• loftool: 0.314
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.77

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.390
• ghis: 0.481

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0893

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Sgcg
• Phenotype: growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype

Gene ontology

• Biological process: muscle organ development;cardiac muscle tissue development;heart contraction
• Cellular component: nucleoplasm;cytoplasm;cytoskeleton;plasma membrane;sarcoglycan complex;integral component of membrane;sarcolemma
• Molecular function: protein binding